Fig. 3

In situ hybridization of genes misregulated in cyclopamine-treated embryos corresponds to direction of expression change on the microarray. A,A2: Nkx3.2 is absent from the jaw joint (black arrowheads), pharyngeal arches (white arrowheads) and notochord (arrow) of cyclopamine-treated embryos. B,B2: Nkx2.2a signal is absent from the floor plate (arrows) and reduced in the brain (arrowheads) of cyclopamine-treated embryos. C,C′,D,D′: Expression of Nkx2.2b (C,C′) and Nkx2.9 (D,D′) is completely lost from brain (arrowheads) and floor plate (arrows) of cyclopamine-treated embryos. E,E′,F,F′: Ventral head expression of Foxf2a (E) and Foxf2b (F) is absent in cyclopamine-treated embryos (E2,F′). G,G2: Tbx20 transcript is decreased in branchiomotor neurons (arrows), but maintains expression in the heart (arrowheads) cyclopamine-treated embryos. H,H′: Ntn1b is decreased in the head (arrowheads) and floor plate (arrows) of cyclopamine-treated embryos. I,I′: Ntn5 is down-regulated in the trunk (arrowheads) of cyclopamine-treated embryos. J,J′: Expression of Fabp11b in the eye (arrowheads) is absent in cyclopamine-treated embryos. K,K′: Urp2 in the floor plate (arrows) is unchanged in cyclopamine-treated embryos. L,L′: Pim1 transcript expression is increased in the brain and eye of cyclopamine-treated embryos. M,M′: Shha shows no change between DMSO and cyclopamine. N,N′: ptch2 is strongly down-regulated in cyclopamine-treated embryos. Scale bars = 100 µm.